Unclear on the concept

As you know, the book Why Intelligent Design Fails:A Scientific Critique of the New Creationism edited by our own Matt Young and Taner Edis http://www2.truman.edu/~edis/books/id/ has just been published. I am one of the authors, with a chapter on the evolution of bacterial flagella. So I feel particularly honoured that one of the first responses to the book is to my chapter.

Unfortunately, the response shows the author is somewhat unclear on the concepts involved.

In the chapter “Evolution of the Bacterial Flagellum” I try, amongst other things, to show a motility system can be built up by cooption of the components of a secretory system to motility functions, it also helps to know that that there are multiple bacterial motility systems, some simple (but now out of date) background can be found at my Evolution of the Bacterial Flagellum page, and an excellent and more exhaustive work is Nic Matzke’s Evolution in (Brownian) space.

For the purposes of this blog though, it is enough to point out that while Dembski and Behe characterize the eubacterial flagella, a swimming motility system, as an “outboard motor”, it is also a secretory system. The secretory system is a key part of flagella function. The flagellar secretory system is also the structure that rotates, and the flagellar secretory system is homologous to the type III secretion system (TTSS) that pathogenic bacteria use to secrete proteins necessary to invade eukaryotic cells. Indeed, place flagella side by side with TTSS and it is hard to tell them apart. In many ways, a TTSS is a flagellum without a motor. Phylogenetic analysis show that TTSS and flagella share a common ancestor, and most workers in the field think that flagella evolved from a primitive secretory system.

One of these is a secretory TTSS, one is a flaellum, but which one?

The question is why would a motor be added to a TTSS that is secreting without it? It turns out that the motor of the flagellum, MotAB, is a proton pump and is part of a family of proton pumps (TolPQ) that drive secretion in a number of systems. Interestingly, the advential gliding motility system of Myxococcus xanthus (where bacteria glide along surfaces rather than swim freely), is a secretory system driven by a TolPQ family proton pump. It is also of interest that flagella are required for a form of gliding motility called swarming. This suggests a pathway for evolving a swimming motility system from a secretion system via functionally intermediate steps.

This is in clear contrast to the “flagella poofed in one go” model used by Dembski in his calculations. But back to the question, “why would a motor be added to a TTSS that is secreting without it”? Because the proton motor increases secretion efficiency. If you knock out the flagella motor then the flagella is paralysed and flagellar secretion continues, but at reduced rate. This suggests that adding a proton pump to a proto-flagellar TTSS-like secretion system would increases secretion, so that association of a proton pump with the proto-flagella secretion system would be beneficial (and result in a system that could be co-opted for motility).

Now in this paper Wilharm G, et al., Yersinia enterocolitica type III secretion depends on the proton motive force but not on the flagellar motor components MotA and MotB. Infect Immun. 2004 Jul;72(7):4004-9.
a non-flagellar TTSS has been described which also uses a proton-pump to help drive secretion. This is completely consistent with the scenario above, where a proton motor is not essential for secretion, but addition of a proton motor is beneficial as it increases secretion.

Also consistent with my model is the distribution of functional motility systems, which show the functional intermediates postulated by my model.

The Yersina non-flagella TTSS doesn’t use MotAB (and wouldn’t it be cool if it did), but I am willing to bet a copy of Gould’s brick that the proton pump turns out to be a TolPQ related protein (heck what if it turns out to be a homolog of MotAB, wouldn’t that be cool).

. …. shows that, protein secretion by the flagellar system of Yersinia is not affected by a mutation in motAB. This indicates that motility and protein secretion are not linked as they appear to be in bacteria that exhibit gliding motility.

Now, this shows they don’t grasp the model (or indeed what the paper says). The paper confirms an expectation from the flagellar secretion system that addition of a proton motor to a TTSS increases, but is not essential for, secretion. Thus addition of a proton pump to a primitive TTSS would be beneficial, and provide a pre-adaptation which later could be co-opted to provide motility.

The key mistake made is not reading the paper (or abstract) carefully. The secretion is via a non-flagella TTSS, not the flagella, as the ARN author says. The experiment was to find out if non-flagella TTSS co-opted flagella MotAB to help drive secretion. The non-flagella TTSS doesn’t use MotAB, rather some other proton pump. As I said, I’ll bet a copy of Gould’s brick they use a TolPQ derived system. Again, this finding is entirely consistent with my model.

So the entire objection arises because the ARN author didn’t understand the difference between a flagellar TTSS and the non-flagella Ysc TTSS. Lets hope further comments on the book don’t make such basic mistakes.

Note also the discover of proton pump involvement was driven by the hypothesis that flagella non-flagella TTSS share a common ancestor. This is a fruitful hypothesis, and several discoveries have come form investigations based on it (see Blocker A, Komoriya K, Aizawa S. Type III secretion systems and bacterial flagella: insights into their function from structural similarities.Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3027-30). Compare this to the sterility of the Paleyist hypothesis, which has given us no insights to TTSS structure of function at all.

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48 Comments

In the chapter “Evolution of the Bacterial Flagellum” I try, amongst other things, to show a motility system can be built up by cooption of the components of a secretory system to motility functions, it also helps to know that that there are multiple bacterial motility systems,…

And this is exactly where your argument fails.
Imagine that I asked an engineer to go into my garage and build a mousetrap from whatever he could find therein. He would look around and perhaps find some pieces of wood, some springs, various screws and nails and a variety of other parts. He would then choose those parts that might be useful and then he might try different alignments of these parts. He might swap out a smaller spring for a larger, or use a different piece of wood or bend a piece of metal until he had achieved his goal: a device to catch mice. The point is that, while all the parts were co-opted from other functions, at no step in this process was intelligence and insight not a factor. Only by using the strictest application of engineering principles and intelligent insight was the goal achieved. You might be able to show that the parts of the flagellar system have analogs in other processes and systems, but what you cannot show is how they were integrated into a system that uses multiple structures, multiple processes and involves multiple functions, (such as a bacterial flagellum) in such a way that these functions not only support each other, they also support the overall function of the system without invoking insight and intelligence.
Also, if I asked 10 different engineers to do the same thing, do you think I would get 10 identical mousetraps? Or 10 different moustraps, with different designs and parts, but performing the same function?

I’ve often wondered just how closely these flagella are to an “outboard motor” in design. I mean the outboard motor on my boat has hinge upon which the propeller can be turned to steer it. No steering mechanism for the flagella as far as I know. My outboard motor has a reverse gear and the boat can move as readily (if not as quickly) backwards as forwards. Although the flagella can be reversed, it results in a wild random tumbling motion instead. My motor prop has 3 blades balanced around the central shaft, a flagella just one.

I know this sounds a bit picky, but since the same crowd who uses this analogy is so very stringent when it comes to other analogous terms like “junk” DNA, I have to wonder why they’re so forgiving here.

The point is that, while all the parts were co-opted from other functions, at no step in this process was intelligence and insight not a factor.

And this is exactly where your argument fails.

This point is irrelevant. You’re supposed to be showing that there is some step in the process where evolution was not and could not be a factor. That’s the claim after all, that evolution is insufficient to form such bio-structures.

If I use your logic then I have to say that every experiment in science shows that intellegence must be involved in whatever the process is that’s being investigated.

This point is irrelevant. You’re supposed to be showing that there is some step in the process where evolution was not and could not be a factor. That’s the claim after all, that evolution is insufficient to form such bio-structures.

That’s not the claim at all. The claim is that this evolution could not have occurred without intelligent guidance i.e. it could not have occurred by random, accidental processes.

That’s not the claim at all. The claim is that this evolution could not have occurred without intelligent guidance i.e. it could not have occurred by random, accidental processes.

You still have not shown any evidence that blind variation and differential selection is insufficient to produce a flagellum. All you have is a poor analogy and a lot of hand waving. What keeps a secretory system from evolving into a motility system, besides your baseless assertions?

While it is true that a moustrap needs intelligent intervention, a bacterium is not a mousetrap. A moustrap does not self-assemble, nor does it reproduce. Bacteria (and all life for that matter) do both of those of those things, which is why random variation AND natural selection can create “a system that uses multiple structures, multiple processes and involves multiple functions, (such as a bacterial flagellum) in such a way that these functions not only support each other, they also support the overall function of the system”

I think Charlie’s problem is the same as other creationists’ - no imagination. I.e. Charlie cannot imagine how something can happen, hence it cannot happen.
It’s the old argument from personal incredutlity.

Dave S., I agree with your criticsm re the “outboard motor” as an analog to the bacterial flagella. I have no idea who first proposed it as an analogy, but I agree that it isn’t a very useful one at the end of the day except to show that both engineers and evolution have discovered that corkscrew shaped objects can provide a propulsive force in a liquid medium.

If you look at an image of a bacteria with its flagella (or even a sperm with its very different flagella), a motorboat is not the first thing that comes to my mind. It’s more like a snake with a giant head.

Side note: many years ago I remember wandering the basement of Barker Hall and passing Julius Adler’s lab http://www.biochem.wisc.edu/adler/. Someone had posted an eyebrow-raising quote from him on the door: “Cocaine, LSD, morphine, amphetamine … I’ve tried them all.” Of course, the quote was referring to compounds Adler had tested to see whether they had attractant or repellent effects on E.coli chemotaxis!

Also, if I asked 10 different engineers to do the same thing, do you think I would get 10 identical mousetraps? Or 10 different moustraps, with different designs and parts, but performing the same function?

Does this mean that there existed more than one “intelligent designer,” since we see multiple structures that accomplish similar tasks? Are you a polytheist, charlie?

RBH: That is the most coherent discussion of “design theory” I’ve ever read. I have been converted. Hereinafter, I will refer only to multiple designers when discussing the alleged intelligent beings who allegedly designed all the “irreducibly complex” (sic) living organisms that ever existed on Earth.

We can recognize the presence of intelligent input, yet have no knowledge of the nature of that intelligence. That is our situation. Any speculation on these matters is just that: hypothetical speculation. We don’t know if there is one, ten, a hundred or an infinite number of designers. These are the wrong questions to ask.
The right question, the truly interesting question is the origin of the information. Where did the coded sequences in DNA and RNA come from?
Now I notice we have a few physicists here, so they hopefully will see my point. All of the laws of the universe that describe how all types of radiation behave are very complex and difficult to understand, the tendency is to restrict oneself to a limited number of special situations. Each of these “special cases” involves radiation travelling from past to future. It is almost unrecognized that the opposite time-sense is possible. If you look at it wrt Maxwell’s equations, the one is as good as the other. We have come to reject the future to past time-sense out of human convention, often without being aware of it at all. Just like the negative root to Einstein’s equation.
If you accept that nature is parsimonious, as most people seem to, it follows that where possibilities exist, they will be utilized.
Quantum mechanics is no exception to this general rule of physics. Our consideration of only past to future propogation allows only for senescence, or degeneration, not for renewal. Place a candle on the table and light it. After a while, all the wax is consumed and the candle goes out. A clear application of the 2nd law of thermodynamics. But in evolution, this process is clearly reversed. because living organisms increase in organization, rather than decrease. They gain information, rather than lose it over time. It is like a candle that collects molecules of carbon dioxide and water and converts them into candle wax. Now we know that photosynthesis can do this, but that’s another story for another day.
So the question occurs, how did living organisms do this? How did they evolve from simple elements into cells and eventually into multicellular organisms in a universe where the arrow of time requires the opposite to occur? Or does it?
Well, the answer might be quite simple. As weird as it might sound (but only because we are unfamiliar with it, not because it can’t happen), living systems must be able to utilize the reverse time-sense as I explained above, operating backwards in time from future to past. It is the only reasonable explanation. Instead of living systems becoming more disorganized, as we might expect, they could be reacting to quantum signals from the future, making use of information traveling backwards in time from a more organized future, obtaining the information necessary for the development of life and changing disorder into order.
We are asking our questions in a back to front order. But by asking the questions in a front to back order, in a future to past time sense, we approach the ultimate cause, the ultimate source of information, instead of receeding from it.
This path is also fraught with danger. Is this “source” at some particular time-location in the future? I think not. If it were, we would have to consider where it’s information is coming from. This takes us still farther back to…eternity? Here the trail fades and we’re left with only the metaphysical to rescue us from our dilemma.

We can recognize the presence of intelligent input, yet have no knowledge of the nature of that intelligence. That is our situation. Any speculation on these matters is just that: hypothetical speculation. We don’t know if there is one, ten, a hundred or an infinite number of designers. These are the wrong questions to ask.

Well, if we see a toaster, and infer (possibly through testing it to see if it propels boats, supports airplanes, or makes bread turn hot and brown) that it was designed to toast bread, we immediately can make one plausible inference about the designer: it wants toast to be available. That is, we can make at least one plausible inference about the intention of the designer. Similarly, if we look at the E. coli flagellum and conclude that it looks designed, we can plausibly infer that the designing agent wanted bacteria to be able to propel themselves by whipping a flagellum. Extending that, we look at multiple kinds of bacteria motility gizmos and plausibly infer that multiple designers wanted bacteria to propel themselves. Some were of the same school of design: there are various kinds of flagella. Some belonged to the “slipping and sliding” school of design, some to the “pull yourself along withe pseudopods” school of design.

I myself think these are exactly the right kinds of questions to ask if one wants to provide an ID explanation. We explain a human-designed structure in terms of (among other things) the knowledge, skils, abilities, and intentions of the designing agent, and so it must be with putatively designed biological structures and processes. Otherwise there’s no “explanation” beyond “Hey! It’s designed!”

Well, the answer might be quite simple. As weird as it might sound (but only because we are unfamiliar with it, not because it can’t happen), living systems must be able to utilize the reverse time-sense as I explained above, operating backwards in time from future to past. It is the only reasonable explanation. Instead of living systems becoming more disorganized, as we might expect, they could be reacting to quantum signals from the future, making use of information traveling backwards in time from a more organized future, obtaining the information necessary for the development of life and changing disorder into order.

That reminds me of an explanation for clairvoyance (remote psi sensing) I read once in a book I was obliged (don’t ask!) to write a review of for a respectable journal. The book explained clairvoyance by positing that the clairvoyant, “seeing” the remote phenomenon, somehow reached back in time to use telekinesis to alter past events so as to produce the image that the clairvoyant was currently sensing. Thinking about the ontological implications of that make my head hurt.

Well, the answer might be quite simple. As weird as it might sound (but only because we are unfamiliar with it, not because it can’t happen), living systems must be able to utilize the reverse time-sense as I explained above, operating backwards in time from future to past.

Joke’s on us. This guy is a troll.

RBH, I read your multidesigner stuff. It’s funny, but it’s at least as strong as ID. If we can extend the heuristic which lets us recognize human design to assert there’s a designer, then since the heuristic lets us recognize a variety of designers from the skill and variety of the creations, it would stand to reason that there are multiple Intelligent Designers. Kudos for establishing that ID indicates polytheism is warranted.

Place a candle on the table and light it. After a while, all the wax is consumed and the candle goes out. A clear application of the 2nd law of thermodynamics. But in evolution, this process is clearly reversed. because living organisms increase in organization, rather than decrease.

Charlie, this isn’t a very good tactic, I would recommend using it only when the Creationist lurkers are likely to be of the YEC/very uneducated type. A lot of the Creationist lurkers on this blog are likely to have at least rudimentary physics knowledge and realize that the earth is not a closed system.

I don’t think I’m a Creationist lurker (in fact, I know I’m not), but I find Charlie Wagner to be interesting and imaginative, and, well, a lot less insufferable than some of you other folks. Good job, Charlie.

Finally somebody rediscovers my theory! I’ve long held that Bacterial Flaggellums went backwards in time in order to evolve, so entropy would go in the necessary direction. One day I’ll be recognized as having seen through the mysteries which so perplexed my lesser peers at Caltech and MIT, and I will be as a giant.

RBH, no one can argue your contributions are not equal to that of the leading crea-I mean, Intelligent Design Theorists. I think you should submit articles to their magazines, and request a spot on their lecture circuit.

Plus, charlie must have heard about the origin by frameshift mutation of the nylonase protein from a non-protein-coding DNA sequence. A whole new gene, just like that. A bit of variation and selection on the originally crudely-functioning protein, and voila, a much more specific and effective protein that meets the criteria most ID advocates employ.

Place a candle on the table and light it. After a while, all the wax is consumed and the candle goes out. A clear application of the 2nd law of thermodynamics. But in evolution, this process is clearly reversed. because living organisms increase in organization, rather than decrease.

G3 Wrote:

Charlie, this isn’t a very good tactic, I would recommend using it only when the Creationist lurkers are likely to be of the YEC/very uneducated type. A lot of the Creationist lurkers on this blog are likely to have at least rudimentary physics knowledge and realize that the earth is not a closed system.

Bob Flynn Wrote:

I don’t think I’m a Creationist lurker (in fact, I know I’m not), but I find Charlie Wagner to be interesting and imaginative, and, well, a lot less insufferable than some of you other folks. Good job, Charlie.

Never mind Charlie, I must say you were right and I was wrong. Even misrepresenting basic physics is a good tactic. However, with Mr. Flynn we only have a sample size of one, any other non-evolutionists want to weigh in here? Does Charlie have a good tactic, or is knowledge of 2nd law of thermo pervasive enough that most ID proponents would see why his argument is bogus? Charlie is a smart guy, and I’m sure he has seen the responses to the 2nd law arguments, so I’ll go off the assumptiom that he is just trying to dupe the lurkers. Surely his audience isn’t the biologists and other scientists here, because he must realize they have at least had an intro to physics class.

Years ago on Talk.origins i pointed out to a creationist that his argument about the 2nd Law was so general it would rule out the possibility of building a refrigerator. As i recall, he replied that refrigerators don’t count because human beings make ‘em.

Next time you encounter that, Jim, switch to ‘your argument about the second law is so general is would rule out the possibility of ice freezing at night’, ice of course being lower entropy than water. It’s a good thing creationists don’t apply their anti-complexity arguments to anything other than evolution, or they’d be totally verklempt. The sun produces heavy elements from simple hydrogens. Iridium is much more complicated than hydrogen. I guess god must have assembled each one, in Creationland.

Besides, everyone knows the answer is, ice uses the opposite-time-sense solutions to physical laws to run in the direction with increasing entropy. ;-)

The problem, as I see it, is that some of you sound like my car mechanic, Jim.

Jim’s a great guy, but he’ll start yapping about “the fetzer valve near crankshaft is out of line, so you may want a new fuel injector, but for 383 models, this means ..blah, blah, blah.”

So, I say, “Jim, Jim — don’t tell me how the watch was made, just give me the time.”

The point of this blog isn’t to teach creationists with simple statements. It’s more or less where science-oriented people discuss evolution, which can get to be a fairly complicated subject. In fact, when it’s simple, that’s usually because some creationist is repetitively making a creationist argument based on a hoary old simple mistake (information, entropy, “Irreducible Complexity”, and Argument from Incredulity, 99% of the time) and people are trying to dumb it down enough to get through to the guy. Which never works, btw.

The sun produces heavy elements from simple hydrogens. Iridium is much more complicated than hydrogen.

Actually this is quite false. Currently the Sun produces helium and someday will do some heavier elements. Indeed no star (that is not currently a supernova) makes any element with an atomic number greater than that of iron since it takes more energy to make them then the fusion would produce. If a star made them it could not hold itself up against its own gravity and would implode. The heavier elements that exist in the universe have been made by supernova explosions.

I think Charlie’s problem is the same as other creationists’ - no imagination. I.e. Charlie cannot imagine how something can happen, hence it cannot happen.

The problem is not that Charles lacks imagination or even intelligence. The problem is he is not willing to use his imagination in this area since he is to busy using his imagination to come up with excuses not to accept the clear evidence of evolution.

It’s the old argument from personal incredutlity.

Yes. And it is even worse: it is even an incredulity since there is not much left to have any incredulity about on this subject: secretory systems clearly exist outside the context of flagella as do the other pieces required. One would think that the only quasi-logical thing the ID advocates could do would be to argue that it is the secretory systems which could not evolve. And then when that is explained (assuming it has not been done already)…

In any case it’s beside the point. The principal thing going on in the sun is fusion from hydrogen to helium, with a smattering of trace heavier elements due to the thermal distribution. At various stages in star life, they fuse various nuclei to get more complex nuclei. If I wanted to be more specific, I would hang out with the Astro guys over in the Bureau of Mines, but I don’t. The point is, it’s another example of a natural process which converts simple things to more complex things, there are a hundred such examples, and yet creationists usually argue no such thing can happen.

One would think that the only quasi-logical thing the ID advocates could do would be to argue that it is the secretory systems which could not evolve. And then when that is explained (assuming it has not been done already) …

IDers seem to be quite conscious of using terms that are familiar, or at least resonate with the public. “Flagella,” whether vaguely recalled from high school biology or first encountered from the “motor” cartoon, resonates much better than “secretory systems.” Just as “Darwinism” resonates and “Kimurism” doesn’t, even though IDers presumably find the latter even more objectionable.

It helps to imagine under what conditions a man would be swimming at, say, the same Reynolds number as his own sperm. Well you put him in a swimming pool that is full of molasses, and the you forbid him to move any part of his body faster than 1 cm/min. Now imagine yourself in that condition; you’re under the swimming pool in molasses, and now you can only move like the hands of a clock. If under those ground rules you are able to move a few meters in a couple of weeks, you may qualify as a low Reynolds number swimmer.